A semiempirical approach to ligand‐binding affinities: Dependence on the Hamiltonian and corrections

We present a combination of semiempirical quantum‐mechanical (SQM) calculations in the conductor‐like screening model with the MM/GBSA (molecular‐mechanics with generalized Born and surface‐area solvation) method for ligand‐binding affinity calculations. We test three SQM Hamiltonians, AM1, RM1, and PM6, as well as hydrogen‐bond corrections and two different dispersion corrections. As test cases, we use the binding of seven biotin analogues to avidin, nine inhibitors to factor Xa, and nine phenol‐derivatives to ferritin. The results vary somewhat for the three test cases, but a dispersion correction is mandatory to reproduce experimental estimates. On average, AM1 with the DH2 hydrogen‐bond and dispersion corrections gives the best results, which are similar to those of standard MM/GBSA calculations for the same systems. The total time consumption is only 1.3–1.6 times larger than for MM/GBSA. © 2012 Wiley Periodicals, Inc.     

Critical points in heavy ion irradiated untwinned YBa(2)Cu3O(7-delta) crystals

The critical points in untwinned YBa(2)Cu(3)O(7-delta) crystals with dilute columnar defects are investigated. We find a convergence of a first order vortex melting line with an irreversibility line associated with the onset of the Bose glass critical regime at the lower critical point. In addition, we find that columnar defects raise the upper critical point, implying that vortex line meandering is a basic feature controlling its position.     

Carrier envelope phase stabilization of a Yb:KGW laser amplifier

In this paper we report on the active stabilization of the carrier envelope phase (CEP) of a Yb:KGW chirped pulse amplifier laser system seeded by a Yb-doped solid-state Kerr-lens mode-locked oscillator. The regenerative amplifier delivers 180 fs CEP stable pulses of 30 μJ-1 mJ energy at a repetition rate tunable from 1 to 200 kHz. The bandwidth of the feedback loop was extended by a factor of 5 using a specially designed high-pass filter, which resulted in a dramatic decrease of CEP jitter below 0.45 rad after the amplifier.     

Laser Microbeams and Optical Tweezers in Ageing Research

We show how a technique developed within the framework of physics and physical chemistry—in a true interdisciplinary approach—can answer questions in life sciences that are not solvable by using other techniques. Herein, we focus on blood‐pressure regulation and DNA repair in ageing studies. Laser microbeams and optical tweezers are now established tools in many fields of science, particularly in the life sciences. A short glimpse is given on the wide field of non‐age‐research applications in life sciences. Then, optical tweezers are used to show that exerting a vertical pressure on cells representing the inner lining of blood vessels results in bursts of NO liberation concomitant with large changes in cell morphology. Repeated treatment of such human umbilical vein endothelial cells (HUVEC) results in stiffening, a hallmark of manifest high blood pressure, a disease primarily of the elderly. As a second application in ageing research, a laser microbeam is used to induce, with high spatial and temporal resolution, DNA damages in the nuclei of U2OS human osteosarcoma cells. A pairwise study of the recruitment kinetics of different DNA repair proteins reveals that DNA repair starts with non‐homologous end joining (NHEJ), a repair pathway, and may only after several minutes switch to the error‐free homologous recombination repair (HRR) pathway. Since DNA damages—when incorrectly repaired—accumulate with time, laser microbeams are becoming well‐used tools in ageing research.     

Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration

Continuum solvation methods are frequently used to increase the efficiency of computational methods to estimate free energies. In this paper, we have evaluated how well such methods estimate the nonpolar solvation free-energy change when a ligand binds to a protein. Three different continuum methods at various levels of approximation were considered, viz., the polarized continuum model (PCM), a method based on cavity and dispersion terms (CD), and a method based on a linear relation to the solvent-accessible surface area (SASA). Formally rigorous double-decoupling thermodynamic integration was used as a benchmark for the continuum methods. We have studied four protein-ligand complexes with binding sites of varying solvent exposure, namely the binding of phenol to ferritin, a biotin analogue to avidin, 2-aminobenzimidazole to trypsin, and a substituted galactoside to galectin-3. For ferritin and avidin, which have relatively hidden binding sites, rather accurate nonpolar solvation free energies could be obtained with the continuum methods if the binding site is prohibited to be filled by continuum water in the unbound state, even though the simulations and experiments show that the ligand replaces several water molecules upon binding. For the more solvent exposed binding sites of trypsin and galectin-3, no accurate continuum estimates could be obtained, even if the binding site was allowed or prohibited to be filled by continuum water. This shows that continuum methods fail to give accurate free energies on a wide range of systems with varying solvent exposure because they lack a microscopic picture of binding-site hydration as well as information about the entropy of water molecules that are in the binding site before the ligand binds. Consequently, binding affinity estimates based upon continuum solvation methods will give absolute binding energies that may differ by up to 200 kJ/mol depending on the method used. Moreover, even relative energies between ligands with the same scaffold may differ by up to 75 kJ/mol. We have tried to improve the continuum solvation methods by adding information about the solvent exposure of the binding site or the hydration of the binding site, and the results are promising at least for this small set of complexes.     

On multiplicative functions which are additive on sums of primes

Let ${f : \mathbb{N} \to \mathbb{C}}$ be a multiplicative function satisfying f(p ₀) ≠ 0 for at least one prime number p ₀, and let k ≥ 2 be an integer. We show that if the function f satisfies f(p ₁ + p ₂ + . . . + p _k ) = f(p ₁) + f(p ₂) + . . . + f(p _k ) for any prime numbers p ₁, p ₂, . . . ,p _k then f must be the identity f(n) = n for each ${n \in \mathbb{N}}$ . This result for k = 2 was established earlier by Spiro, whereas the case k = 3 was recently proved by Fang. In the proof of this result for k ≥ 6 we use a recent result of Tao asserting that every odd number greater than 1 is the sum of at most five primes.     

Diboraanthracene-Doped Polymer Systems for Colour-Tuneable Room-Temperature Organic Afterglow

Organic ultralong room temperature phosphorescence (RTP), or organic afterglow, is a unique phenomenon, gaining widespread attention due to its far-reaching application potential and fundamental interest. Here, two laterally expanded 9,10-dimesityl-dihydro-9,10-diboraanthracene (DBA) derivatives are demonstrated as excellent afterglow materials for red and blue-green light emission, which is traced back to persistent thermally activated delayed fluorescence and RTP. The lateral substitution of polycyclic DBA scaffold, together with weak transversal electron-donating mesityl groups, ensures the optimal molecular properties for (reverse) intersystem crossing and long-lived triplet states in a rigid poly(methyl methacrylate) matrix. The achieved afterglow emission quantum yields of up to 3 % and 15 %, afterglow lifetimes up to 0.8 s and 3.2 s and afterglow durations up to 5 s and 25 s (for red and blue-green emitters, respectively) are attributed to the properties of single molecules.